A single gene produces two different proteins, utilizing different exons. What is the most likely explanation?

  Differences in mRNA splicing.

Explanation:

The exon is the region of a gene that is not separated during the cutting and splicing process and thus remains in the mature messenger RNA. In genes encoding a protein, it is the exons which contain the information to produce the protein encoded in the gene. In these cases, each exon encodes a specific portion of the complete protein, so that the set of exons forms the coding region of the gene. In eukaryotes, the exons of a gene are separated by long regions of DNA (called introns) which do not code.

RNA splicing is a post-transcriptional process of maturing RNA from which certain sequential fragments are removed. This process is very common in eukaryotes, and can occur in any type of RNA, although it is more common in mRNA. It consists of removing the introns from the primary transcript and then binding the exons. Particularly, alternative RNA splicing takes place when one gene can produce different proteins as a result of what segments are considered as introns and exons. When different segments are considered exons, the result is a great diversity of mature transcripts which produce different proteins.

So, gene splicing is a post-transcriptional modification in which a gene can code for many proteins, which makes it an important source of protein diversity.